Výsledky vyhledávání - Phylogeny Computer algorithms. Algorithms.

Fast error-tolerant quartet phylogeny algorithms Autor Brown, Daniel G., Truszkowski, Jakub

“…We present a quartet-based phylogeny algorithm that returns the correct topology for n taxa in O(nlogn…”
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An experimental phylogeny to benchmark ancestral sequence reconstruction Autor Randall, Ryan N., Radford, Caelan E., Roof, Kelsey A., Natarajan, Divya K., Gaucher, Eric A.

“… One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation…”
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A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood Autor Guindon, Stéphane, Gascuel, Olivier, Rannala, Bruce

“…The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods…”
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A new method to cluster genomes based on cumulative Fourier power spectrum Autor Dong, Rui, Zhu, Ziyue, Yin, Changchuan, He, Rong L., Yau, Stephen S.-T.

“…Analyzing phylogenetic relationships using mathematical methods has always been of importance in bioinformatics. Quantitative research may interpret the raw…”
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Areas of Endemism: An Improved Optimality Criterion Autor Szumik, Claudia A., Goloboff, Pablo A., Linder, Peter

“… to it. Algorithms to evaluate areas of endemism under this criterion are discussed, and implemented in a computer program (NDM; available at www.zmuc.dk/public/phylogeny). The new algorithms allow evaluation of much larger data sets…”
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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0 Autor Guindon, Stéphane, Dufayard, Jean-François, Lefort, Vincent, Anisimova, Maria, Hordijk, Wim, Gascuel, Olivier

“…PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology…”
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Models, algorithms and programs for phylogeny reconciliation Autor Doyon, Jean-Philippe, Ranwez, Vincent, Daubin, Vincent, Berry, Vincent

“…Gene sequences contain a gold mine of phylogenetic information. But unfortunately for taxonomists this information does not only tell the story of the species…”
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Phylogeny of caucasian rock lizards (Darevskia) and other true lizards based on mitogenome analysis: Optimisation of the algorithms and gene selection Autor Murtskhvaladze, Marine, Tarkhnishvili, David, Anderson, Cort L., Kotorashvili, Adam

“…We generated a phylogeny for Caucasian rock lizards (Darevskia), and included six other families of true lizards (Lacertini…”
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FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program Autor Lefort, Vincent, Desper, Richard, Gascuel, Olivier

“…FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of Neighbor Joining (NJ…”
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Cladograms with Path to Event (ClaPTE): A novel algorithm to detect associations between genotypes or phenotypes using phylogenies Autor Handelman, Samuel K, Aaronson, Jacob M., Seweryn, Michal, Voronkin, Igor, Kwiek, Jesse J., Sadee, Wolfgang, Verducci, Joseph S., Janies, Daniel A.

“…Associations between genotype and phenotype provide insight into the evolution of pathogenesis, drug resistance, and the spread of pathogens between hosts…”
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Fast Dating Using Least-Squares Criteria and Algorithms Autor To, Thu-Hien, Jung, Matthieu, Lycett, Samantha, Gascuel, Olivier

“…Abstract Phylogenies provide a useful way to understand the evolutionary history of genetic samples, and data sets with more than a thousand taxa are becoming increasingly common, notably with viruses (e.g…”
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Towards Resolving the Complete Fern Tree of Life Autor Lehtonen, Samuli

“… The availability of large molecular data sets together with efficient computer algorithms, now enables us to reconstruct evolutionary histories with previously unseen completeness…”
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PhISCS-BnB: a fast branch and bound algorithm for the perfect tumor phylogeny reconstruction problem Autor Sadeqi Azer, Erfan, Rashidi Mehrabadi, Farid, Malikić, Salem, Li, Xuan Cindy, Bartok, Osnat, Litchfield, Kevin, Levy, Ronen, Samuels, Yardena, Schäffer, Alejandro A, Gertz, E Michael, Day, Chi-Ping, Pérez-Guijarro, Eva, Marie, Kerrie, Lee, Maxwell P, Merlino, Glenn, Ergun, Funda, Sahinalp, S Cenk

“… Principled approaches to tumor phylogeny reconstruction via SCS data are typically based on general computational methods for solving an integer linear program, or a constraint satisfaction program…”
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Stability of SARS-CoV-2 phylogenies Autor Turakhia, Yatish, De Maio, Nicola, Thornlow, Bryan, Gozashti, Landen, Lanfear, Robert, Walker, Conor R., Hinrichs, Angie S., Fernandes, Jason D., Borges, Rui, Slodkowicz, Greg, Weilguny, Lukas, Haussler, David, Goldman, Nick, Corbett-Detig, Russell

“…The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately…”
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Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm Autor Löytynoja, Ari, Vilella, Albert J., Goldman, Nick

“…Motivation: Accurate alignment of large numbers of sequences is demanding and the computational burden is further increased by downstream analyses depending on…”
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Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees Autor Kenah, Eben, Britton, Tom, Halloran, M. Elizabeth, Longini, Ira M.

“… A phylogeny can increase the precision of these estimates by providing partial information about who infected whom…”
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Many-core algorithms for statistical phylogenetics Autor Suchard, Marc A., Rambaut, Andrew

“… Here, we describe novel algorithms and methods for evaluating phylogenies under arbitrary molecular evolutionary models on graphics processing units (GPUs…”
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A Binary Particle Swarm Algorithm with A Simple Mutation Operator for Solving Phylogenies Problems Autor Alsrraj, Reem

“…Manipulating a huge amount of data sets makes the mechanism of searching very difficult to find the bestfeatures combinations in phylogenetic tree…”
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Harnessing machine learning to guide phylogenetic-tree search algorithms Autor Azouri, Dana, Abadi, Shiran, Mansour, Yishay, Mayrose, Itay, Pupko, Tal

“… In this proof-of-concept study, we train a machine-learning algorithm over an extensive cohort of empirical data to predict the neighboring trees that increase the likelihood, without actually…”
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Polyphest: fast polyploid phylogeny estimation Autor Yan, Zhi, Cao, Zhen, Nakhleh, Luay

“… complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS…”
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